RE: [Joelib-help] aromaticity in SD files

[Wayne V. <vol...@re...>]

bondPairs is a HashMap.  The intent is to make sure that an aromatic
atom is involved in at most one double-bond.  If an atom has not
participated in a double-bond and an aromatic atom it is attached to
also has not participated in a double-bond, then bondType is set to 2.
Both atoms are then added to the bondPairs HashMap, with the target of
one atom's HashMap pointing to the other atom.

If what I wrote it correct at all, though, it could just be a
java.util.HashSet I guess.  Doesn't need to be a HashMap.

> -----Original Message-----
> From: Joerg K. Wegner [mailto:we...@in...]
> Sent: Monday, December 15, 2003 8:12 AM
> To: Wayne Volkmuth
> Cc: Joe...@li...
> Subject: Re: [Joelib-help] aromaticity in SD files
>=20
> Hi Wayne,
>=20
> what contains the 'bondPairs'-variable ? Seems to be a HashMap or
> something related, but what's their content.
>=20
> Regards, Joerg
>=20
> > Hi Joerg,
> >
> > A couple weeks ago I asked about the bond type "4" in the sd files
> > produced by JOELib.  You said
> >
> >
> >>ah, o.k., but that's not a bug that's a feature! These bonds are
> >>aromatic and you will find this also in the SD-FILE definition of
MDL.
> >>That why you should use JOELib or OpenBabel, because they have a
> >> really
> >>great chemical expert system behind 'simple' file conversion. Only
if
> >>you know aromatic atoms/bonds you can create e.g. a MOL2 file !!!
> >
> >
> > I went and looked at the sd file definition on the mdl web site.  A
bond
> > type of "4" is only permitted (required?) for structures intended
for
> > use as queries (against, presumably, a database).  I'm sure you'll
find
> > that particular distinction as odd as I do but at any rate, that's
their
> > standard.
> >
> >>From what I've seen JOELib seems to be focused on representing
specific,
> > rather than generic (i.e. query), molecules so it seems as though
the sd
> > writer should put out alternating 1's and 2's.  Or perhaps it's
sensible
> > to have behavior depend on a flag, so you can ask the sd writer to
use
> > type "4" bonds if desired.
> >
> > Here's a fragment of code that I think will do the trick.  Let me
know
> > what you think.
> >
> > Wayne
> >
> >                     //check, if aromatic bond
> >                     if (atom.isAromatic() && nbr.isAromatic() ||
> > (bond.getBO() =3D=3D JOEBond.JOE_AROMATIC_BOND_ORDER))
> >                     {
> >                         //  Non-query structures must use Kekule
> > representation
> >                         if (bondPairs.containsKey(new
> > Integer(atom.getIdx())) || bondPairs.containsKey(new
> > Integer(nbr.getIdx())))
> >                         {
> >                             bondType =3D 1; // single bond
> >                         }
> >                         else
> >                         {
> >                             bondType =3D 2; // double bond
> >                             bondPairs.put(new
Integer(atom.getIdx()),
> > new Integer(nbr.getIdx()));
> >                             bondPairs.put(new Integer(nbr.getIdx()),
new
> > Integer(atom.getIdx()));
> >                         }
> >                     }
> >                     else
> >                     {
> >                         // 1 single
> >                         // 2 double
> >                         bondType =3D bond.getBO();
> >                     }
> >
> >
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>=20
>=20
> --
> Dipl. Chem. Joerg K. Wegner
> Center of Bioinformatics Tuebingen (ZBIT)
> Department of Computer Architecture
> Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
> Phone: (+49/0) 7071 29 78970
> Fax: (+49/0) 7071 29 5091
> E-Mail: mailto:we...@in...
> WWW:    http://www-ra.informatik.uni-tuebingen.de
> --
> Never mistake motion for action.
>                           E. Hemingway
>=20


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